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- PDB-6st7: Crystal Structure of Domain Swapped Trp Repressor V58I Variant wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6st7 | |||||||||||||||||||||
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Title | Crystal Structure of Domain Swapped Trp Repressor V58I Variant with bound L-trp | |||||||||||||||||||||
![]() | Trp operon repressor | |||||||||||||||||||||
![]() | DNA BINDING PROTEIN / HOSTAL / L-trp binding / Domain swapping | |||||||||||||||||||||
Function / homology | ![]() sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Sprenger, J. / Lawson, C.L. / Carey, J. / Drouard, F. / von Wachenfeldt, C. / Schulz, A. / Linse, S. / Lo Leggio, L. | |||||||||||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() Title: Crystal structures of Val58Ile tryptophan repressor in a domain-swapped array in the presence and absence of L-tryptophan. Authors: Sprenger, J. / Lawson, C.L. / von Wachenfeldt, C. / Lo Leggio, L. / Carey, J. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.6 KB | Display | ![]() |
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PDB format | ![]() | 42.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 366.8 KB | Display | ![]() |
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Full document | ![]() | 366.9 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Data in CIF | ![]() | 7.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6st6SC ![]() 7os9C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 12206.979 Da / Num. of mol.: 1 / Mutation: V58I Source method: isolated from a genetically manipulated source Details: The actual sequence is that from the Uniprot entry P0A881 but with V58I mutation Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: trpR, rtrY, b4393, JW4356 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-TRP / |
#3: Chemical | ChemComp-IPA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.15 Å3/Da / Density % sol: 76.11 % / Description: bi-pyramidal, hexagonal |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM Na HEPES, 100 mM sodium chloride, 27.5-35%(v/v) isopropanol, pH 7.5 PH range: 7-8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→45.57 Å / Num. obs: 9881 / % possible obs: 99.9 % / Redundancy: 10.49 % / Biso Wilson estimate: 81.02 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.0627 / Rrim(I) all: 0.0658 / Net I/σ(I): 17.52 |
Reflection shell | Resolution: 2.45→2.54 Å / Rmerge(I) obs: 0.2095 / Num. unique obs: 1543 / CC1/2: 0.434 / Rrim(I) all: 0.2198 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6ST6 Resolution: 2.45→43.41 Å / SU ML: 0.4127 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.8651 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 96.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→43.41 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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